During the opening days of the invasion of Afghanistan, Tier 1 operators of a Navy SEAL squad from DEVGRU, call sign Neptune, composed of operators code-named Mother, Voodoo, Preacher and Rabbit are sent to meet with an Afghan informant named Tariq, who has intelligence that the CIA is interested in retrieving. Neptune is ambushed by Taliban forces, and fights their way through the village to recover Tariq. Shortly after extraction, Tariq informs them that the Taliban and Al-Qaeda have a significant force composed of 500 to 1,000 combatants in the Shah-i-Kot Valley. Neptune is tasked to secure Bagram Airfield with a contingent of ANA soldiers. By March 2002, the airfield is re-purposed as a forward operating base by NATO forces. U.S. Army Colonel Drucker commands all local assets, is shown as a cautious, competent officer, in contrast to his commanding officer, General Flagg, who works in an office in the United States and is ignorant of the AFO teams' role in the operation. While Drucker plans to use Tier 1 operators to reconnoiter insurgent positions in the valley and ANA soldiers to eliminate them, Flagg is mistrusting of the locals and gives the Colonel a 24-hour deadline to deploy the 10th Mountain Division, the 101st Airborne Division, and U.S. Army Rangers.
Meanwhile, Tier 1 teams are inserted into the area to perform reconnaissance and coordinate fire support. AFO Wolfpack, consisting of four Delta Force operators code-named Panther, Vegas, Deuce and Dusty eliminate enemy positions in two small villages and travel to their observation point "Clementine" while Neptune does the same to "OP Dorothy". After completing their mission ahead of schedule, Drucker sends ANA soldiers to eliminate several insurgent positions. Flagg calls in a rage, and unknowingly orders an AC-130U crew to open fire on friendly forces. The surviving ANA forces panic and withdraw, leaving the Colonel no choice but to deploy the Rangers as ordered. During insertion into the Sha-i-kot Valley, the Rangers come under heavy fire and a Chinook is shot down. The Rangers are pinned down by heavy machine guns, so a fireteam led by Sergeant Patterson consisting of Specialist Dante Adams, Corporal Hernandez and US Air Force Enlisted Terminal Attack Controller (ETAC) Tech Sergeant Ybarra flank the enemy positions and destroy the machine guns. They move to secure another landing zone, but are ambushed by insurgents, who arrive in overwhelming numbers. Surrounded, and running out of ammunition, Ybarra radios Bagram for reinforcements, which arrive in the form of a pair of AH-64 Apaches, facilitating the Rangers’ extraction. The Apaches move though the mountains destroying a Taliban armory and enemy mortar positions. As they return to base, a Taliban Anti-Aircraft Gun attempts to destroy the helicopters, however, the gunner is killed by Deuce.
Deuce and Dusty move up the mountains and ambush enemy patrols and mortar teams, providing sniper support for Neptune, who is in heavy contact on the adjacent mountain, Takur Ghar. Neptune withdraws over the ridge line, and fights their way to the extraction point. Mother and Rabbit make it to the helicopter, but the Chinook lifts off early due to heavy enemy fire, leaving Voodoo and Preacher behind. Defying orders to return to base, Mother and Rabbit re-insert, barely escaping death when their Chinook comes under fire. They evade hostile patrols while searching for Voodoo and Preacher. However, the two operators are eventually compromised and forced to jump off a cliff in an attempt to escape, with Rabbit sustaining multiple gunshot wounds in the process. Both suffer injuries and are captured by insurgents. Back at Bagram, Colonel Drucker attempts to organize forces to extract Neptune. Wolfpack is too far to provide assistance. General Flagg refuses to risk additional losses, and only assigns a AC-130U gunship, which can only stay on station for 15 more minutes. Drucker defies orders and sends in a Ranger Quick Reaction Force to extract Neptune.
The Chinook is hit by heavy fire, three Rangers and a crew member are killed, and four more are injured. After securing the crash site for the wounded and medics, Hernandez, Ybarra, Adams and Patterson head for the mountain pass. Hernandez is wounded while attempting to find an entrance of a spider-hole and Ybarra brings him back to the landing zone. Adams and Patterson link up with Preacher and Voodoo and continue searching for Mother and Rabbit. After the four of them together assaulted two enemy strongholds with the help of a CIA Predator drone, they eventually locate the two missing operators tied up in a remote bunker, who were tortured by the insurgents. Rabbit is dying as his teammates evacuate him. The team calls for extraction, however, the nearest helicopters are flying from Kandahar, many miles away. Rabbit's condition worsens while his squad-mates try to keep him awake. However, moments before the extraction helicopter arrives, Rabbit finally succumbs to his wounds. The seven survivors are safely extracted, along with the remaining Ranger QRF. While observing a pair of F-15Es bombing the remaining insurgent bunkers, Preacher collects a rabbit's foot charm from Rabbit’s corpse, with Mother and Preacher noting that the war is far from over.
The game ends with a scene of two undercover operatives, sitting on a street in a Middle Eastern town, conversing with each other in the Pashto dialect. As they converse about the quality of the tea they are drinking, they identify a man they are looking out for and stand to approach him.
